LAMMPS (12 Jun 2025 - Development - patch_12Jun2025-605-g5eb61491f0-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread.
  using 1 OpenMP thread(s) per MPI task
# May 2025
# Test script for MD-KMC accelerated diffusion testing in LAMMPS
# Created by Jacob Tavenner, Baylor University

# Initiation -------------------------------------
units           metal
dimension       3
boundary        p p p
atom_style      atomic

# Atom Definition --------------------------------
lattice fcc 3.762
Lattice spacing in x,y,z = 3.762 3.762 3.762
region          whole block 0 1 0 1 0 1
create_box      2 whole
Created orthogonal box = (0 0 0) to (3.762 3.762 3.762)
  1 by 1 by 1 MPI processor grid
create_atoms    1 region whole
Created 4 atoms
  using lattice units in orthogonal box = (0 0 0) to (3.762 3.762 3.762)
  create_atoms CPU = 0.000 seconds

replicate 6 16 6
Replication is creating a 6x16x6 = 576 times larger system...
  orthogonal box = (0 0 0) to (22.572 60.192 22.572)
  1 by 1 by 1 MPI processor grid
  2304 atoms
  replicate CPU = 0.000 seconds

region      puck block INF INF 7 9 INF INF
set         region puck type 2
Setting atom values ...
  360 settings made for type

# Force Fields -----------------------------------
pair_style      meam
pair_coeff      * * library_2nn.meam Mo Co Ni V Fe Al Cr MoCoNiVFeAlCr_2nn.meam Ni Cr
Reading MEAM library file library_2nn.meam with DATE: 2024-08-08
Reading MEAM potential file MoCoNiVFeAlCr_2nn.meam with DATE: 2024-08-08

# Settings ---------------------------------------
timestep        0.002
thermo          100

# Computations -----------------------------------
compute         voroN all voronoi/atom neighbors yes

run             0
WARNING: No fixes with time integration, atoms won't move
For more information see https://docs.lammps.org/err0028 (src/verlet.cpp:60)
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 6.8
  ghost atom cutoff = 6.8
  binsize = 3.4, bins = 7 18 7
  2 neighbor lists, perpetual/occasional/extra = 2 0 0
  (1) pair meam, perpetual
      attributes: full, newton on
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
  (2) pair meam, perpetual, half/full from (1)
      attributes: half, newton on
      pair build: halffull/newton
      stencil: none
      bin: none
Per MPI rank memory allocation (min/avg/max) = 13.32 | 13.32 | 13.32 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   0             -9674.3728      0             -9674.3728     -212400.94    
Loop time of 8.62e-07 on 1 procs for 0 steps with 2304 atoms

0.0% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0          | 0          | 0          |   0.0 |  0.00
Neigh   | 0          | 0          | 0          |   0.0 |  0.00
Comm    | 0          | 0          | 0          |   0.0 |  0.00
Output  | 0          | 0          | 0          |   0.0 |  0.00
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 8.62e-07   |            |       |100.00

Nlocal:           2304 ave        2304 max        2304 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           4735 ave        4735 max        4735 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:          99072 ave       99072 max       99072 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:       198144 ave      198144 max      198144 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 198144
Ave neighs/atom = 86
Neighbor list builds = 0
Dangerous builds = 0
thermo_style    custom step temp press pxx pyy pzz lx ly lz vol pe

# Execution --------------------------------------

velocity    all create 2400 908124 loop geom
fix         temp all npt temp 1000 1000 1000 aniso 0 0 1
fix         mc all neighbor/swap 50 12 1340723 1000 3 voroN diff 2
thermo_style    custom step temp press pxx pyy pzz lx ly lz vol pe f_mc[*]
#dump           dump2 all custom 5000 dump.edge-3_Ni-Cr.* id type x y z c_eng c_csym

run 1000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- fix neighbor/swap command: doi:10.1016/j.commatsci.2022.111929

@Article{Tavenner2023111929,
 author = {Jacob P. Tavenner and Mikhail I. Mendelev and John W. Lawson},
 title = {Molecular dynamics based kinetic Monte Carlo simulation for accelerated diffusion},
 journal = {Computational Materials Science},
 year = {2023},
 volume = {218},
 pages = {111929}
 url = {https://dx.doi.org/10.1016/j.commatsci.2022.111929}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Per MPI rank memory allocation (min/avg/max) = 13.32 | 13.32 | 13.32 Mbytes
   Step          Temp          Press           Pxx            Pyy            Pzz             Lx             Ly             Lz           Volume         PotEng        f_mc[1]        f_mc[2]    
         0   2400          -187517.52     -187464.28     -188202.86     -186885.42      22.572         60.192         22.572         30667.534     -9674.3728      0              0            
       100   1687.1584      13681.454      14112.794      14026.902      12904.667      21.637683      57.728817      21.63703       27027.2       -9600.6424      24             23           
       200   1578.9879     -6074.2872     -7170.074      -4456.4001     -6596.3875      21.71812       58.13626       21.712735      27414.722     -9569.7632      48             44           
       300   1586.0502      1921.5002      2871.8396      1449.0001      1443.661       21.677891      58.13829       21.643595      27277.759     -9572.2349      72             67           
       400   1599.8151      459.13309     -890.62191      638.40686      1629.6143      21.662475      58.208733      21.64368       27291.495     -9576.3711      96             88           
       500   1622.7406     -980.83045     -358.66202     -2883.0275      299.19813      21.627475      58.244052      21.683194      27313.708     -9583.2244      120            110          
       600   1558.3072      661.01491      2134.4817     -1069.4315      917.99455      21.675158      58.08722       21.705367      27328.136     -9564.1953      144            132          
       700   1585.7908      2896.8915      2712.2516      5131.3298      847.09324      21.703761      57.89964       21.704281      27274.466     -9572.077       168            154          
       800   1593.7707     -754.08728     -529.51328      807.24585     -2539.9944      21.682927      58.129291      21.67599       27320.704     -9574.7174      192            175          
       900   1594.1026     -504.80889      147.79949     -1421.9393     -240.28691      21.678023      58.172814      21.655846      27309.572     -9574.7989      216            198          
      1000   1604.8161      1017.6914      707.59987      2068.9348      276.53957      21.696786      57.985179      21.676799      27271.408     -9578.0587      240            221          
Loop time of 30.6062 on 1 procs for 1000 steps with 2304 atoms

Performance: 5.646 ns/day, 4.251 hours/ns, 32.673 timesteps/s, 75.279 katom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 27.514     | 27.514     | 27.514     |   0.0 | 89.90
Neigh   | 0.22106    | 0.22106    | 0.22106    |   0.0 |  0.72
Comm    | 0.011786   | 0.011786   | 0.011786   |   0.0 |  0.04
Output  | 0.00030095 | 0.00030095 | 0.00030095 |   0.0 |  0.00
Modify  | 2.854      | 2.854      | 2.854      |   0.0 |  9.32
Other   |            | 0.004794   |            |       |  0.02

Nlocal:           2304 ave        2304 max        2304 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           4744 ave        4744 max        4744 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         130039 ave      130039 max      130039 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs:       260078 ave      260078 max      260078 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 260078
Ave neighs/atom = 112.88108
Neighbor list builds = 62
Dangerous builds = 0

#write_data     pulse_center.data
Total wall time: 0:00:30
